Lucy DNA sequence quality and vector trimming tool



Lucy was designed and written at The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute), and it has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses.  The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method.  As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers.


Lucy is available in the form of a software download only.  I currently have no plans to create an open-source community development project for lucy.  If you think that would be valuable, please contact me about it.  In the meantime, the download package includes the full source code, so feel free to customize it for your environment.


You can download the lucy distribution from our SourceForge,net project page.


Lucy is described in the following publication:


Hui-Hsien Chou and Michael H. Holmes (2001) DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093-1104.


One of the authors of lucy has developed Lucy2, which adds a GUI interface to lucy.  It is available separately, here:


(Note that Lucy2 is not included with the lucy download package.)